In a new study published in Alimentary Pharmacology & Therapeutics, researchers at the University of Alberta's faculty of medicine and dentistry have shown that a betaretrovirus which resembles a mouse mammary tumor virus infects patients with the rare liver disease, primary biliary cirrhosis (PBC).

Ed Rybicki's insight:

OK, it's from February, but this is quite a big deal: proof that a human retrovirus seems to be implicated in a serious human disease.

Adenoviruses are a ubiquitous group of viruses that have been found in a wide range of hosts. A novel adenovirus from a skunk suffering from acute hepatitis was isolated and its DNA genome sequenced. The analysis revealed this virus to be a new member of the genus Mastadenovirus, with a genome of 31,848 bp in length containing 30 genes predicted to encode proteins, and with a G+C content of 49.0%. Global genomic organization indicated SkAdV-1 was similar in organization to bat and canine adenoviruses, and phylogenetic comparison suggested these viruses shared a common ancestor. SkAdV-1 demonstrated an ability to replicate in several mammalian liver cell lines suggesting a potential tropism for this virus.

Our Special Issue aims to celebrate and highlight the integration of these two fields of research, Proteomics and Virology, as well as to raise awareness in both communities of the opportunities present in Viral Proteomics research. The issue contains 15 manuscripts that reflect the impressive diversity of virology studies that benefit from the wide range of available proteomic-based approaches. The elegant merge of these two fields of research is illustrated by the fact that these manuscripts come from both virology and mass spectrometry laboratories. While, of course, not all of the leading laboratories were able to contribute to this issue, we are very pleased to say that, as detailed below, the investigators highlighted in this issue represent some of the major supporters of proteomics for virology studies. We have organized this issue using classical virology taxonomy by dividing the issue into two main sections communicating reports describing either DNA or RNA viruses and a third section on non-MS based proteomics.

The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus-host interactions precludes accurate prediction of their roles and impacts. Here we mined publicly available bacterial and archaeal genomic datasets to identify 12,498 high‑confidence viral genomes linked to their microbial hosts. These data augment public datasets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7-38% of 'unknown' sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that ( i ) 264 new viral genera were identified (doubling known genera) and ( ii ) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and co‑infection prevalences, as well as evaluation of in silico virus-host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes.

With the genomes of Ötzi, the 5300-year-old iceman, and even Neandertals pouring out of DNA sequencing labs lately, you might think that it’s now a piece of cake to glean the entire genetic code of an ancient human. But it turns out that those studies used exceptionally pure samples of DNA taken from human bone, tooth, hair, or other tissue typically preserved in frozen soil, ice, or a chilly cave. More often, human remains found by scientists have been sitting in soil warm enough to harbor bacteria, which swamp out the human DNA with their genes and make it too costly to analyze. A clever new method for purifying ancient human DNA samples—reported here last week at the annual meeting of the American Society of Human Genetics—could change that, however.

The average ancient DNA sample taken from, say, a human tooth or bone is often less than 1% short, degraded pieces of human DNA; the rest is bacterial DNA. Although scientists could sequence this gemisch, they would have to run the samples through their sequencing machines many times to zoom in on the human DNA portion, and it’s not worth the cost. Instead, researchers often prepare stretches of modern human DNA that roughly match the genes or sequences they’re interested in and use these so-called probes to filter the sample. (Modern and ancient human DNA are similar enough that the probes will stick to the ancient DNA.) But this is still expensive, and it reveals the sequence of only a subset of the genome.

A team at Stanford University has now come up with a better idea.

Postdoctoral researcher Meredith Carpenter and others in the lab of Carlos Bustamante made their probes from RNA instead of DNA, which is “super cheap,” Bustamante says. They found a way to make enough RNA probes to cover the entire genome of an average modern human. The probe has a chemical group that sticks to special beads, so when the researchers mix the probes with an ancient DNA sample, they can wash away the nonhuman DNA. The final step is to use an RNA-chewing enzyme to get rid of the probes, leaving only pure ancient human DNA that can then be fed into a genome sequencing machine.

When the researchers tested this filtering method on a dozen ancient bone, teeth, and hair DNA samples from 500 to 3500 years old, they gleaned twofold to 13-fold more human genetic sequence from the samples than they could have by simply sequencing the mixture the same number of times. This higher resolution yielded new information about the samples. For instance, while previously they could only say that a more than 2500-year-old Bronze Age tooth from Bulgaria was European, they could now narrow its ethnic origin down to central or southern European. The team was also able to determine that a more than 500-year-old Peruvian mummy did not have European ancestry, as Spanish explorers claimed.

The first human inhabitants of the Americas lived in a time thousands of years before the first written records, and the story of their transcontinental migration is the subject of ongoing debate and active research. A study by multi-institutional, international collaboration of researchers, published this week in Science (DOI: 10.1126/science.aab3884) presents strong evidence, gleaned from ancient and modern DNA samples, that the ancestry of all Native Americans can be traced back to a single migration event, with subsequent gene flow between some groups and populations that are currently located in East Asia and Australia.

The human virome plays important roles in health and immunity. However, current methods for detecting viral infections and antiviral responses have limited throughput and coverage. Here, we present VirScan, a high-throughput method to comprehensively analyze antiviral antibodies using immunoprecipitation and massively parallel DNA sequencing of a bacteriophage library displaying proteome-wide peptides from all human viruses. We assayed over 108 antibody-peptide interactions in 569 humans across four continents, nearly doubling the number of previously established viral epitopes. We detected antibodies to an average of 10 viral species per person and 84 species in at least two individuals. Although rates of specific virus exposure were heterogeneous across populations, antibody responses targeted strongly conserved “public epitopes” for each virus, suggesting that they may elicit highly similar antibodies. VirScan is a powerful approach for studying interactions between the virome and the immune system.

This method allows comprehensive analysis of antiviral antibodies in human sera. VirScan combines DNA microarray synthesis and bacteriophage display to create a uniform, synthetic representation of peptide epitopes comprising the human virome. Immunoprecipitation and high-throughput DNA sequencing reveal the peptides recognized by antibodies in the sample. The color of each cell in the heatmap depicts the relative number of antigenic epitopes detected for a virus (rows) in each sample (columns).

When reporting research findings, scientists document the steps they followed so that others can verify and build upon the research. When those steps have been described in sufficient detail that others can retrace the steps and obtain similar results, the research is said to be reproducible. Computers play a vital role in many research disciplines and present both opportunities and challenges for reproducibility. Computers can be programmed to execute analysis tasks, and those programs can be repeated and shared with others. Due to the deterministic nature of most computer programs, the same analysis tasks, applied to the same data, will often produce the same outputs. However, in practice, computational findings often cannot be reproduced, due to complexities in how software is packaged, installed, and executed—and due to limitations in how scientists document analysis steps. Many tools and techniques are available to help overcome these challenges. Here we describe six such strategies. With a broad scientific audience in mind, we describe strengths and limitations of each approach, as well as circumstances under which each might be applied. No single strategy is sufficient for every scenario; thus we emphasize that it is often useful to combine approaches.

Scientists at Columbia University's Mailman School of Public Health and the School of Public Health of Li Ka Shing Faculty of Medicine at the University of Hong Kong have shown for the first time that it is possible to predict the timing and intensity of influenza outbreaks in subtropical climates like Hong Kong where flu seasons can occur at different times and more than once during a year. Results appear online in the journal PLOS Computational Biology.

Ed Rybicki's insight:

Interesting stuff: because flu is far less seasonal in the tropics and subtropics.

African horse sickness virus (AHSV), a member of the Orbivirus genus in the family Reoviridae, is an arthropod-transmitted pathogen that causes a devastating disease in horses with a mortality rate greater than 90%. Fundamental research on AHSV and the development of safe, efficacious vaccines could benefit greatly from an uncomplicated genetic modification method to generate recombinant AHSV. We demonstrate that infectious AHSV can be recovered by transfection of permissive mammalian cells with transcripts derived in vitro from purified AHSV core particles.

Direct delivery of aerosolized vaccines to the respiratory mucosa elicits both systemic and mucosal responses. This vaccine strategy has not been tested for Ebola virus (EBOV) or other hemorrhagic fever viruses. Here, we examined the immunogenicity and protective efficacy of an aerosolized human parainfluenza virus type 3–vectored vaccine that expresses the glycoprotein (GP) of EBOV (HPIV3/EboGP) delivered to the respiratory tract. Rhesus macaques were vaccinated with aerosolized HPIV3/EboGP, liquid HPIV3/EboGP, or an unrelated, intramuscular, Venezuelan equine encephalitis replicon vaccine expressing EBOV GP. Serum and mucosal samples from aerosolized HPIV3/EboGP recipients exhibited high EBOV-specific IgG, IgA, and neutralizing antibody titers, which exceeded or equaled titers observed in liquid recipients. The HPIV3/EboGP vaccine induced an EBOV-specific cellular response that was greatest in the lungs and yielded polyfunctional CD8+ T cells, including a subset that expressed CD103 (αE integrin), and CD4+ T helper cells that were predominately type 1. The magnitude of the CD4+ T cell response was greater in aerosol vaccinees. The HPIV3/EboGP vaccine produced a more robust cell-mediated and humoral immune response than the systemic replicon vaccine. Moreover, 1 aerosol HPIV3/EboGP dose conferred 100% protection to macaques exposed to EBOV. Aerosol vaccination represents a useful and feasible vaccination mode that can be implemented with ease in a filovirus disease outbreak situation.

Middle East Respiratory Syndrome coronavirus (MERS-CoV) causes severe respiratory disease with a high mortality rate. There is no licensed vaccine or antiviral for MERS. Here we isolated for the first time, to our knowledge, a potent MERS-CoV–neutralizing antibody from memory B cells of an infected individual. This antibody binds to a novel site on the viral Spike protein, neutralizes by interfering with the binding to the cellular receptor CD26, and is highly effective both in prophylaxis and in therapy in a relevant mouse model. This antibody can be developed for prophylaxis, for postexposure prophylaxis, or for the treatment of severe MERS-CoV infections.

Latest in the law of unintended consequences is the finding of a rising number of malaria deaths in Guinea as patients avoided treatment centers, fearing either being quarantined among those afflicted with Ebola, or being mistreated.A new study in The Lancet Infectious Diseases shows that the deaths from malaria are likely to greatly exceed the total number of deaths caused by Ebola itself.

There were an estimated 74,000 fewer cases of malaria seen in Guinea healthcare facilities, as outpatient attendance dropped almost in half. As lead author, Dr. Mateusz Plucinski (of the CDC and President’s Malaria Initiative) explained, “One problem is that the early symptoms of malaria (fever, headache, and body aches) mimic those of Ebola virus disease…Malaria is one of the main causes of fever and health facilities visits in Guinea, but our data suggest that since the start of the Ebola epidemic people with fevers have avoided clinics for fear of contracting Ebola or being sent to an Ebola treatment centre.” Interestingly, this treatment drop extended to districts without any reported Ebola cases.

Molluscum contagiosum virus (MCV) is the only known extant human-adapted poxvirus. It causes a persistent infection by dampening the immune response against infected skin lesions, but the mechanism is unknown. Brady et al. report the discovery of MC132, a new MCV immune antagonist that binds and targets NF-κB p65, a key regulator of antiviral immunity and inflammation, for degradation using a strategy that is strikingly similar to that used by some gammaherpesvirus proteins. This research sheds additional light on how MCV evades human immunity to persist in the skin.

Sharing your scoops to your social media accounts is a must to distribute your curated content. Not only will it drive traffic and leads through your content, but it will help show your expertise with your followers.

Integrating your curated content to your website or blog will allow you to increase your website visitors’ engagement, boost SEO and acquire new visitors. By redirecting your social media traffic to your website, Scoop.it will also help you generate more qualified traffic and leads from your curation work.

Distributing your curated content through a newsletter is a great way to nurture and engage your email subscribers will developing your traffic and visibility.
Creating engaging newsletters with your curated content is really easy.